House Speaker John Boehner praised the ruling, saying it's "further proof that President Obama's health care law is completely unworkable. It cannot be fixed."

Earnest said that the ruling would not immediately affect Americans currently receiving tax credits through the federal exchange, adding that he expects the Department of Justice to fight the decision. Acting for the Obama administration, the DoJ will likely ask for the full U.S. Court of Appeals for the District of Columbia Circuit to weigh in on a ruling made by a three-judge panel, Earnest said.

When asked if a DoJ defeat would spell doom for the Affordable Care Act, Earnest side-stepped the question, repeating that the administration is "confident in the legal basis that supports our case."

He spoke after a federal appeals court panel declared that government subsidies worth billions of dollars that helped 4.7 million people buy insurance on HealthCare.gov are illegal.

In a 2-1 ruling, the panel said such subsidies can be granted only to those people who bought insurance in an Obamacare exchange run by an individual state or the District of Columbia—not on the federally run exchange HealthCare.gov.

In a statement, Boehner said the GOP-dominated House would pursue a lawsuit against Obamacare. "The president has demonstrated he believes he has the power to make his own laws," the Ohio Republican said. "That's not the way our system of government was designed to work."